8SNK | pdb_00008snk

Crystal structure of metformin hydrolase (MfmAB) from Pseudomonas mendocina sp. MET-2 mutant (MfmA/D188N)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	A0A2S0XPN7
in silico model	AlphaFold	A0A316GGX0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	1 uL 10 mg/mL protein + 1 uL 20% w/v PEG3350, 0.1 M Bis-Tris propane, 0.2 M NaNO3, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.7	α = 90
b = 162.3	β = 101.1
c = 152.7	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2022-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.85	80	99.2	0.998	10.48	4.5067		207175

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.95	99.8		0.936	2.81

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.85	19.753	206742	10338	99.247	0.19	0.1882	0.2	0.2227	0.23	29.003

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.614		-0.785	-2.13		1.694

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.455
r_dihedral_angle_3_deg	16.205
r_dihedral_angle_2_deg	9.49
r_lrange_it	7.138
r_lrange_other	7.012
r_dihedral_angle_1_deg	6.871
r_scangle_it	5.485
r_scangle_other	5.484
r_mcangle_it	3.859
r_mcangle_other	3.859
r_scbond_other	3.694
r_scbond_it	3.693
r_mcbond_it	2.957
r_mcbond_other	2.956
r_angle_refined_deg	1.646
r_angle_other_deg	0.592
r_nbd_refined	0.217
r_symmetry_nbd_other	0.198
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.165
r_nbd_other	0.154
r_symmetry_xyhbond_nbd_refined	0.129
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.063
r_bond_refined_d	0.01
r_metal_ion_refined	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15438
Nucleic Acid Atoms
Solvent Atoms	1453
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building